I can identify with fighting the interface, as I had a similar experience when I first started: I was moving from using Emacs, and there are certainly things I miss and habits that were hard to form. Breakpoints inside Eclipse/EPIC just don't work properly: you're pretty much stuck with using an external debugger, which EPIC (thankfully) lets you configure. This is one of my biggest complaints with Eclipse.

I am curious which version of Eclipse you had these experiences with: if it was a few versions ago, I think you'll find the Eclipse team (and the EPIC team, for that matter) have put a lot of work into making the overall experience more pleasant. There's still a ways to go, but it's a pretty interesting project. They've been very responsive to my comments about usability. The EPIC team would probably be interested in Perl-specific comments you might have. Anything you get them to improve will be a welcome help for me. :)

I hadn't used Komodo in a while, and just checked out the most recent version of that, as well -- they've fixed a lot of what I had an issue with, and the performance seems quite a bit better as well. Still, neither Eclipse or Komodo gets pulled out for quick scripts, because they're still slower to load and run than Emacs or SciTE (though the latter sees less use from me, lately, as I've moved to Mac for development, and there still isn't an OSX port).